Shipping industry and seaborne trade have rapidly increased over the last fifty years, mainly due to the continuous increasing demand for chemicals and fuels. Consequently, despite current regulations, the occurrence of accidental spills poses an important risk. Hazardous and noxious substances (HNSs) have been raising major concern among environmental managers and scientific community for their heterogeneity, hazardous potential towards aquatic organisms and associated social-economic impacts. A literature review on ecotoxicological hazards to aquatic organisms was conducted for seven HNSs: acrylonitrile, n-butyl acrylate, cyclohexylbenzene, hexane, isononanol, trichloroethylene and xylene. Information on the mechanisms of action of the selected HNS was also reviewed. The main purpose was to identify: i) knowledge gaps in need of being addressed in future research; and ii) a set of possible biomarkers suitable for ecotoxicological assessment and monitoring in both estuarine and marine systems. Main gaps found concern the scarcity of information available on ecotoxicological effects of HNS towards marine species and their poorly understood mode of action in wildlife. Differences were found between the sensitivity of freshwater and seawater organisms, so endpoints produced in the former may not be straightforwardly employed in evaluations for the marine environment. The relationship between sub-individual effects and higher level detrimental alterations (e.g. behavioural, morphological, reproductive effects and mortality) are not fully understood. In this context, a set of biomarkers associated to neurotoxicity, detoxification and anti-oxidant defences is suggested as potential indicators of toxic exposure/effects of HNS in marine organisms. Overall, to support the development of contingency plans and the establishment of environmental safety thresholds, it will be necessary to undertake targeted research on HNS ecotoxicity in the marine environment. Research should address these issues under more realistic exposure scenarios reflecting the prevailing spatial and temporal variability in ecological and environmental conditions.